ELECTROCHEMICAL MEASUREMENT OF THE SOLVENT ACCESSIBILITY OF NUCLEOBASES USING ELECTRON-TRANSFER BETWEEN DNA AND METAL-COMPLEXES

Oxidizing metal complexes mediate the electrochemical oxidation of guanine nucleotides in polymeric DNA and oligonucleotides. This catalysis results in an enhancement in cyclic voltammograms that yields the rate constant for oxidation of guanine by the metal complex via digital simulation. The rate constant for oxidation of guanine in calf thymus DNA by Ru(bpy)(3)(3+) is 9.0 x 10(3) M(-1) s(-1). which has been confirmed in separate experiments utilizing pulsed voltammetry and stopped-flow spectrophotometry. The rate constant depends linearly on the driving force with a slope of 1/2, as predicted by Marcus theory. Formation of the double helix precludes direct collision of the metal complex with the guanine residue, which imposes a finite distance of solvent through which the electron must tunnel. This distance is dependent on the presence of the oxidized guanine in a mismatch, which decreases the tunneling distance as assessed from electron-transfer theory. The oxidation rate constants therefore follow the trend G (single strand) > GA > GG > GT > GC. These mismatches are all distinguishable from one another, providing a new basis for probing small changes in the solvent accessibility of guanine that may be useful in DNA sequencing or quantitatively mapping complex nucleic acid structures.